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Installation

T3 was only tested on Linux (Ubuntu_ 22.04.1 LTS) and MacOS. We don't expect it to work on Windows.

It can be installed on a server, as well as on your local desktop / laptop, in order to submit jobs to the server/s.

Package Manager and Cloning from Github

Unix-like platforms

1. Install curl or wget

You can install either package.

Option 1

bash sudo apt install curl

Option 2

bash sudo apt install wget

2. Install compiler

  • Ubuntu or Debian

    bash sudo apt install git gcc g++ make

  • Fedora or Red Hat

    bash sudo dnf install git gcc gcc-c++ make

3. Download Python Package Manager

Option 1
curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
bash Mambaforge-$(uname)-$(uname -m).sh
Option 2
wget "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
bash Mambaforge-$(uname)-$(uname -m).sh

4. Clone T3 Repository

Clone T3's repository by typing the following command in the desired folder (e.g., under ~/Code/):

git clone https://github.com/ReactionMechanismGenerator/T3.git

Setting up Path

  • To set up T3 to your local path in .bashrc, you have two options:

Option 1

Terminal Command (NOTE: Make sure to change "~/Path/to/T3/" accordingly"):

bash echo 'PYTHONPATH=$PYTHONPATH:~/Path/to/T3/' >> ~/.bashrc

Option 2

Editing .bashrc directly (NOTE: Make sure to change "~/Path/to/T3/" accordingly"):

  • In terminal, enter the command:

bash sudo gedit ~/.bashrc

  • Then in the opened file, on a new line, enter the following:

text export PYTHONPATH=$PYTHONPATH:~/Path/to/T3/

Install dependencies

T3 requires RMG-Py, RMG-databse and ARC to function correctly. In order to install the necessary dependencies, you can follow either option below.

Option 1

  • Navigate to the T3 folder, depending on where you cloned it to.

  • Open a terminal in the T3 folder, and type the following:

bash make install all

Note: This can take some time to finish.

  • You have now installed all the required dependencies.

Option 2

  • Install the latest versions of RMG-Py and the RMG-database on the same machine where T3 is installed. Follow the instructions on RMG's Documentation.

  • Make sure to install RMG's developer version which includes important recent features. Note that the installation instructions suggest Anaconda, but Mambaforge can be used in it's place.

  • Be sure to add RMG-Py to your PATH and PYTHONPATH as explained in the instructions.

  • Install the latest version of ARC on the same machine where T3 is installed. Follow the instructions on ARC's documentation

  • Make sure to add ARC to your PATH and PYTHONPATH, as well as to define your servers as explained in ARC's documentation.

  • Create the Anaconda/Mambaforge environment for T3 by executing the following command in the T3 folder:

$ mamba env create -f environment.yml

INFO:     Collecting package metadata (repodata.json): done
INFO:     Solving environment: done
INFO:     
INFO:     Downloading and Extracting Packages
INFO:     ...
INFO:     Preparing transaction: done
INFO:     Verifying transaction: done
INFO:     Executing transaction: done
INFO:     #
INFO:     # To activate this environment, use
INFO:     #
INFO:     #     $ conda activate t3_env
INFO:     #
INFO:     # To deactivate an active environment, use
INFO:     #
INFO:     #     $ conda deactivate
  • Activate the T3 environment every time before running T3:

bash conda activate t3_env

Add T3 aliases to your .bashrc

Some optional yet convenient aliases are listed below (make sure to change "/Path/to/T3/" accordingly). Add these to your .bashrc file, which can be edited by typing, e.g., sudo nano ~/.bashrc:

export t3_path=$HOME`/Path/to/T3'
alias t3e='conda activate t3_env'
alias t3='python $t3_path/T3.py input.yml'
alias t3code='cd $t3_path'

Then, after sourcing .bashrc or restarting the terminal, simply typing t3e will activate the environment, typing t3code will change the directory into the T3 repository, and finally typing t3 from any folder with a valid T3 input file will execute T3 in that folder.

Updating T3

The T3 repository is being updated frequently. Make sure to update your instance of T3 to enjoy new features and get recent bug fixes. To get the most recent developer version, execute the following commands (make sure to change ~/Path/to/T3/ accordingly:

cd ~/Path/to/T3/
git fetch origin
git pull origin main

The above will update your main branch of T3.